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haplotype analysis

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https://www.readbyqxmd.com/read/29029226/new-insights-into-the-genetic-basis-of-monge-s-disease-and-adaptation-to-high-altitude
#1
Tsering Stobdan, Ali Akbari, Priti Azad, Dan Zhou, Orit Poulsen, Otto Appenzeller, Gustavo F Gonzales, Amalio Telenti, Emily H M Wong, Shubham Saini, Ewen F Kirkness, J Craig Venter, Vineet Bafna, Gabriel G Haddad
Human high-altitude (HA) adaptation or mal-adaptation is explored to understand the physiology, pathophysiology and molecular mechanisms that underlie long-term exposure to hypoxia. Here we report the results of an analysis of the largest whole-genome-sequencing of Chronic Mountain Sickness (CMS) and non-CMS individuals, identified candidate genes and functionally validated these candidates in a genetic model system (Drosophila). We used PreCIOSS algorithm that uses Haplotype Allele Frequency score to separate haplotypes carrying the favored allele from the non-carriers and accordingly prioritize genes associated with the CMS or non-CMS phenotype...
September 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029143/genome-wide-analysis-of-genetic-risk-factors-for-rheumatic-heart-disease-in-aboriginal-australians-provides-support-for-pathogenic-molecular-mimicry
#2
Lesley-Ann Gray, Heather A D'Antoine, Steven Y C Tong, Melita McKinnon, Dawn Bessarab, Ngaire Brown, Bo Reményi, Andrew Steer, Genevieve Syn, Jenefer M Blackwell, Michael Inouye, Jonathan R Carapetis
Background: Rheumatic heart disease (RHD) following Group A Streptococcus (GAS) infections is heritable and prevalent in Indigenous populations. Molecular mimicry between human and GAS proteins triggers pro-inflammatory cardiac valve-reactive T-cells. Methods: Genome-wide genetic analysis was undertaken in 1263 Aboriginal Australians (398 RHD cases; 865 controls). Single nucleotide polymorphisms (SNPs) were genotyped using Illumina HumanCoreExome BeadChips. Direct typing and imputation was used to fine-map the human leukocyte antigen (HLA) region...
September 26, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29029121/clinical-heterogeneity-and-phenotypic-expansion-of-napi-iia-associated-disease
#3
Korcan Demir, Melek Yildiz, Hilla Bahat, Michael Goldman, Nisreen Hassan, Shay Tzur, Ayala Ofir, Daniella Magen
Context: NaPi-IIa, encoded by SLC34A1 is a key phosphate transporter in the mammalian proximal tubule, and plays a cardinal role in renal phosphate handling. NaPi-IIa impairment has been linked to various overlapping clinical syndromes, including hypophosphatemic nephrolithiasis with osteoporosis, renal Fanconi's syndrome with chronic kidney disease, and most recently, with idiopathic infantile hypercalcemia and nephrocalcinosis. Objectives: We studied the molecular basis of idiopathic infantile hypercalcemia with partial proximal tubulopathy in two apparently unrelated patients of Israeli and Turkish descent...
September 29, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29029038/geographical-distance-and-local-environmental-conditions-drive-the-genetic-population-structure-of-a-freshwater-microalga-bathycoccaceae-chlorophyta-in-patagonian-lakes
#4
Leonardo D Fernández, Cristián E Hernández, M Romina Schiaffino, Irina Izaguirre, Enrique Lara
The patterns and mechanisms underlying the genetic structure of microbial populations remain unresolved. Herein we investigated the role played by two non-mutually exclusive models (i.e. isolation by distance and isolation by environment) in shaping the genetic structure of lacustrine populations of a microalga (a freshwater Bathycoccaceae) in the Argentinean Patagonia. To our knowledge, this was the first study to investigate the genetic population structure in a South American microorganism. Population-level analyses based on ITS1-5...
October 3, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29028986/a-new-haplotype-block-detection-method-for-dense-genome-sequencing-data-based-on-interval-graph-modeling-of-clusters-of-highly-correlated-snps
#5
Sun Ah Kim, Chang-Sung Cho, Suh-Ryung Kim, Shelley B Bull, Yun Joo Yoo
Motivation: Linkage disequilibrium (LD) block construction is required for research in population genetics and genetic epidemiology, including specification of sets of single nucleotide polymorphisms (SNPs) for analysis of multi-SNP based association and identification of haplotype blocks in high density sequencing data. Existing methods based on a narrow sense definition do not allow intermediate regions of low LD between strongly associated SNP pairs and tend to split high density SNP data into small blocks having high between-block correlation...
September 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29026722/mthfr-3-untranslated-region-polymorphisms-contribute-to-recurrent-pregnancy-loss-risk-and-alterations-in-peripheral-natural-killer-cell-proportions
#6
Eun Sun Kim, Jung Oh Kim, Hui Jeong An, Jung Hyun Sakong, Hyun Ah Lee, Ji Hyang Kim, Eun Hee Ahn, Young Ran Kim, Woo Sik Lee, Nam Keun Kim
OBJECTIVE: To identify the associations between polymorphisms of the 3'-untranslated region (UTR) of methylenetetrahydrofolate reductase (MTHFR) gene, which codes for an important regulatory enzyme primarily involved in folate metabolism, and idiopathic recurrent pregnancy loss (RPL) in Korean women. METHODS: The study population comprised 369 RPL patients and 228 controls. MTHFR 2572C>A, 4869C>G, 5488C>T, and 6685T>C 3'-UTR polymorphisms were genotyped by polymerase chain reaction-restriction fragment length polymorphism analysis or by TaqMan allelic discrimination assays...
September 2017: Clinical and Experimental Reproductive Medicine
https://www.readbyqxmd.com/read/29025896/high-throughput-single-molecule-telomere-characterization
#7
Jennifer McCaffrey, Eleanor Young, Katy Lassahn, Justin Sibert, Steven Pastor, Harold Riethman, Ming Xiao
We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7-bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG)n tract length at the end of each large telomere-terminal DNA segment...
October 12, 2017: Genome Research
https://www.readbyqxmd.com/read/29025590/identification-of-pathogenic-retrotransposon-insertions-in-cancer-predisposition-genes
#8
Yaping Qian, Debora Mancini-DiNardo, Thaddeus Judkins, Hannah C Cox, Krystal Brown, Maria Elias, Nanda Singh, Courtney Daniels, Jayson Holladay, Bradford Coffee, Karla R Bowles, Benjamin B Roa
Cancer risks have been previously reported for some retrotransposon element (RE) insertions; however, detection of these insertions is technically challenging and very few oncogenic RE insertions have been reported. Here we evaluate RE insertions identified during hereditary cancer genetic testing using a comprehensive testing strategy. Individuals who had single-syndrome or pan-cancer hereditary cancer genetic testing from February 2004 to March 2017 were included. RE insertions were identified using Sanger sequencing, Next Generation Sequencing, or multiplex quantitative PCR, and further characterized using targeted PCR and sequencing analysis...
October 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29024003/molecular-characterization-of-the-llama-fgf5-gene-and-identification-of-putative-loss-of-function-mutations
#9
M S Daverio, L Vidal-Rioja, E N Frank, F Di Rocco
Llama, the most numerous domestic camelid in Argentina, has good fiber-production ability. Although a few genes related to other productive traits have been characterized, the molecular genetic basis of fiber growth control in camelids is still poorly understood. Fibroblast growth factor 5 (FGF5) is a secreted signaling protein that controls hair growth in humans and other mammals. Mutations in the FGF5 gene have been associated with long-hair phenotypes in several species. Here, we sequenced the llama FGF5 gene, which consists of three exons encoding 813 bp...
October 11, 2017: Animal Genetics
https://www.readbyqxmd.com/read/29023858/interleukin-1-gene-cluster-haplotype-analysis-in-the-chronic-outcome-prediction-of-the-hepatitis-b-virus-infection
#10
Bita Javan, Mohamad Reza Kalani, Majid Shahbazi
Hepatitis B virus (HBV) infection is well known as an important cause of the chronic liver disease. The screening of the genotype of certain cytokines might be helpful to predict the clinical outcome of an HBV infection. The present study investigates the relationship between the polymorphism and haplotypes of the Interleukin-1 (IL-1) gene family, including IL-1-alpha (IL-1A), IL-1-beta (IL-1B) and IL-1 receptor antagonist (IL-1RN), with chronic HBV infection. 297 chronic HBV and 333 matched on sex and age control individuals were genotyped using the standard sequence-specific- polymerase chain reaction primer (SSP-PCR) method...
October 11, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/29022495/genetic-polymorphisms-of-hotair-gene-are-associated-with-the-risk-of-breast-cancer-in-a-sample-of-southeast-iranian-population
#11
Shekoufeh Hassanzarei, Mohammad Hashemi, Hedieh Sattarifard, Seyed Mehdi Hashemi, Gholamreza Bahari, Saeid Ghavami
There is an increasing body of evidence which highlights the critical functions of long non-coding RNAs in the carcinogenicity mechanism of a variety of cancers. It has been reported that HOX transcript antisense intergenic RNA, a member of long non-coding RNA family, increases breast cancer risk. To date, no data regarding the association between HOX transcript antisense intergenic RNA polymorphisms and the risk of breast cancer development has been reported in Iran. Here, we examine the possible association between HOX transcript antisense intergenic RNA gene polymorphisms and breast cancer in a sample of southeast Iranian female population...
October 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29022486/association-of-vitamin-d-receptor-gene-polymorphisms-with-breast-cancer-risk-in-an-egyptian-population
#12
Haidan M El-Shorbagy, Nada H Mahmoud, Salwa Sabet
This study aimed to explore whether genetic polymorphisms in vitamin D receptor are correlated to the breast cancer prevalence in an Egyptian population. Polymerase chain reaction-restriction fragment polymorphism was used to genotype three frequently analyzed vitamin D receptor gene single-nucleotide polymorphisms (rs1544410, rs7975232, and rs731236) and were identified by sequencing analysis. This is the first study that recorded a new single-nucleotide polymorphism in ApaI genotype within an Egyptian population and was registered with the accession number KY859868...
October 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29020875/founder-effect-of-the-ret-c611y-mutation-in-multiple-endocrine-neoplasia-2a-in-denmark-a-nationwide-study
#13
Jes Sloth Mathiesen, Jens Peter Kroustrup, Peter Vestergaard, Kirstine Stochholm, Per Løgstrup Poulsen, Åse Krogh Rasmussen, Ulla Feldt-Rasmussen, Mette Gaustadnes, Torben Falck Ørntoft, Maria Rossing, Finn Cilius Nielsen, Anders Albrechtsen, Kim Brixen, Christian Godballe, Anja Lisbeth Frederiksen
BACKGROUND: Multiple endocrine neoplasia (MEN) 2A and 2B are caused by REarranged during Transfection (RET) germline mutations. In a recent nationwide study we reported of an unusually high prevalence (33%) of families with the C611Y mutation and hypothesized that this might be due to a founder effect. We conducted the first nationwide study of haplotypes in MEN2A families aiming to investigate the relatedness and occurrence of de novo mutations among Danish families carrying similar mutations...
October 12, 2017: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/29020097/nuclear-and-mtdna-phylogenetic-analyses-clarify-the-evolutionary-history-of-two-species-of-native-hawaiian-bats-and-the-taxonomy-of-lasiurini-mammalia-chiroptera
#14
Amy B Baird, Janet K Braun, Mark D Engstrom, Ashlyn C Holbert, Maritza G Huerta, Burton K Lim, Michael A Mares, John C Patton, John W Bickham
Previous studies on genetics of hoary bats produced differing conclusions on the timing of their colonization of the Hawaiian Islands and whether or not North American (Aeorestes cinereus) and Hawaiian (A. semotus) hoary bats are distinct species. One study, using mtDNA COI and nuclear Rag2 and CMA1, concluded that hoary bats colonized the Hawaiian Islands no more than 10,000 years ago based on indications of population expansion at that time using Extended Bayesian Skyline Plots. The other study, using 3 mtDNA and 1 Y-chromosome locus, concluded that the Hawaiian Islands were colonized about 1 million years ago...
2017: PloS One
https://www.readbyqxmd.com/read/29020049/further-insight-into-genetic-variation-and-haplotype-diversity-of-cherry-virus-a-from-china
#15
Rui Gao, Yunxiao Xu, Thierry Candresse, Zhen He, Shifang Li, Yuxin Ma, Meiguang Lu
Cherry virus A (CVA) infection appears to be prevalent in cherry plantations worldwide. In this study, the diversity of CVA isolates from 31 cherry samples collected from different orchards around Bohai Bay in northeastern China was analyzed. The complete genome of one of these isolates, ChYT52, was found to be 7,434 nt in length excluding the poly (A) tail. It shares between 79.9-98.7% identity with CVA genome sequences in GenBank, while its RdRp core is more divergent (79.1-90.7% nt identity), likely as a consequence of a recombination event...
2017: PloS One
https://www.readbyqxmd.com/read/29018314/experimental-infection-of-different-tomato-genotypes-with-tomato-mosaic-virus-led-to-a-low-viral-population-heterogeneity-in-the-capsid-protein-encoding-region
#16
Nina Sihelská, Zuzana Vozárová, Lukáš Predajňa, Katarína Šoltys, Martina Hudcovicová, Daniel Mihálik, Ján Kraic, Michaela Mrkvová, Otakar Kúdela, Miroslav Glasa
The complete genome sequence of a Slovak SL-1 isolate of Tomato mosaic virus (ToMV) was determined from the next generation sequencing (NGS) data, further confirming a limited sequence divergence in this tobamovirus species. Tomato genotypes Monalbo, Mobaci and Moperou, respectively carrying the susceptible tm-2 allele or the Tm-1 and Tm-2 resistant alleles, were tested for their susceptibility to ToMV SL-1. Although the three tomato genotypes accumulated ToMV SL-1 to similar amounts as judged by semi-quantitative DAS-ELISA, they showed variations in the rate of infection and symptomatology...
October 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28993831/association-of-snps-haplotypes-in-promoter-of-tnf-a-and-il-10-gene-together-with-life-style-factors-in-prostate-cancer-progression-in-indian-population
#17
Kapil Bandil, Pallavi Singhal, Atika Dogra, Sudhir K Rawal, D C Doval, Anil K Varshney, Mausumi Bharadwaj
OBJECTIVE: Levels of proinflammatory (TNF A) and anti-inflammatory (IL-10) cytokines play a key role in the progression of inflammation as well as cancer disease. We were investigating the potential association of single-nucleotide polymorphisms (SNPs)/haplotypes in proinflammatory (TNF A) and anti-inflammatory (IL-10) cytokines locus with the development of PCa in Indian population. MATERIALS AND METHODS: We had genotyped 235 BPH/PCa samples (130 BPH and 105 cancer) along with 115 control samples for proinflammatory (TNF A -238G/A and -308G/A) and anti-inflammatory (IL-10 -1082A/G, -819C/T and -592C/A) cytokines SNPs in the gene promoter region using ARMS-PCR method...
October 9, 2017: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://www.readbyqxmd.com/read/28993188/the-effect-of-killer-cell-immunoglobulin-like-receptor-genotype-on-outcome-of-hematopoietic-stem-cell-transplantation-from-matched-sibling
#18
Sally M Elfishawi, Ghada I Mossallam, Raafat Abd El-Fattah, Alaa El-Haddad, Azza M Kamel
The alloreactivity of natural killer (NK) cell after allogeneic hematopoietic stem cell transplantation (AHSCT) is regulated by the interaction between donor killer immunoglobulin-like receptors (KIRs) and recipient human leukocyte antigen (HLA)- class I molecules. The aim was to identify KIR genes, haplotypes and their HLA-class I ligands and to investigate their association with transplantion outcome. The study included 65 patient/donor pairs who received AHSCT from HLA-matched identical siblings. KIR genotyping was done for donors using reverse sequence specific oligonucleotide probes (rSSO) coupled with luminex technology, while HLA-C genotyping was performed in patients using rSSO strip assay...
October 6, 2017: Human Immunology
https://www.readbyqxmd.com/read/28990350/association-of-dnmt3b-gene-variants-with-sporadic-parkinson-s-disease-in-a-chinese-han-population
#19
Xiang Chen, Yousheng Xiao, Lei Wei, Yijuan Wu, Jianjun Lu, Wenyuan Guo, Shuxuan Huang, Miaomiao Zhou, Mingshu Mo, Zhe Li, Luan Cen, Shaomin Li, ChaohaoYang, Zhuohua Wu, Sophie Hu, Zhong Pei, XinLing Yang, Shaogang Qu, Pingyi Xu
INTRODUCTION: Parkinson's disease (PD) is the second most common neurodegenerative disorder worldwide. Epigenetic modifications, specifically DNA methylation, have been implicated in the development of this disease. Genetic variants of DNA methyltransferase 3b (DNMT3b), one of the most important DNA methyltransferases, were shown to be associated with PD in a Brazilian population. However, it is unclear whether genetic variants of DNMT3b increase the risk of PD in the Chinese Han people...
October 9, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28989979/haplotype-based-association-analysis-of-general-cognitive-ability-in-generation-scotland-the-english-longitudinal-study-of-ageing-and-uk-biobank
#20
David M Howard, Mark J Adams, Toni-Kim Clarke, Eleanor M Wigmore, Yanni Zeng, Saskia P Hagenaars, Donald M Lyall, Pippa A Thomson, Kathryn L Evans, David J Porteous, Reka Nagy, Caroline Hayward, Chris S Haley, Blair H Smith, Alison D Murray, G David Batty, Ian J Deary, Andrew M McIntosh
BACKGROUND: Cognitive ability is a heritable trait with a polygenic architecture, for which several associated variants have been identified using genotype-based and candidate gene approaches. Haplotype-based analyses are a complementary technique that take phased genotype data into account, and potentially provide greater statistical power to detect lower frequency variants. METHODS: In the present analysis, three cohort studies (n total = 48,002) were utilised: Generation Scotland: Scottish Family Health Study (GS:SFHS), the English Longitudinal Study of Ageing (ELSA), and the UK Biobank...
2017: Wellcome Open Research
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